Legacy of the Alicorns
by packleader96
Summary: Three months had passed since the coronation of Twilight Sparkle, and she has been having trouble adjusting to her new life and responsibilities, but when strange events begin to occur, it's up to her and a strange new ally to stop it, and learn the truth about the Alicorn race, before everything she knows fall apart, Rated T for Language, Violence, and Some Sexuality.
1. prologue

**A/N: here it is, my first story that is based off the season 3 finale, had some spare time, and decided to start writing this story, anyway, hope you enjoy.**

**Disclaimer: I don't own anything, aside from my OC's, everything else belongs to its respectful owner's.**

**Legacy of the Alicorn's: prologue**

It was a bright sunny day over the kingdom of Equestria, as everypony did their daily jobs, much of the kingdom, was still adjusting to their newly crowned, Princess Twilight Sparkle.

Her coronation was celebrated all across the kingdom, it had now been three months since that great day, and she was trying to adjust to the life of a Princess and an alicorn, despite being a part of the royal family, Celestia granted her permission to remain in PonyVille with her friends, and only to be called to Canterlot, when she was needed.

But there was something coming, something, not even the Princesses could expect, something that could change Equestria forever.

(Everfree forest)

The stallion opened his eyes, and saw nothing but darkness, he found himself lying on his stomach, as his eyes started to refocus, he looked around, and saw himself lying inside some sort of cave, he pushed himself up on to his hooves, when he felt a sharp pain in his head, he placed his hoof on his head and began rubbing, trying to dull the pain.

After his eyes had fully adjusted, he looked around again, he couldn't remember anything, how he got there, "where am I?" he asked out loud, half expecting for somepony to answer, but he heard nothing, he saw a light coming from the far end of the tunnel, he could tell it was sunlight, and he began making his way there, his body felt weak, his throat was dry, and his stomach growled, as he walked, multiple times had had almost tripped and fell.

As he got closer he saw it was the exit to the cave, as he made his way faster over there, he came to the end of the tunnel, and walked out into the sunlight, the first look made him cover his eyes from the brightness, but his eyes soon adjusted, and he looked up into the sky, and saw it was bright blue, and dotted with white puffy clouds, he looked around him and saw nothing but thick tree's, the tree's mad either area around him seem dark and menacing, but he still couldn't remember how he got there, or why he was there.

He saw what appeared to be a broken tree branch in front of him, he looked up and saw what appeared to be a broken tree limb, and he decided to get a better view.

Luckily for him, he was unlike any other pony, he was not a unicorn, or a Pegasus, or even an earth pony, he was an alicorn, with a pair of wings and a horn, his name was Rising Star.

Despite feeling weak, he spread his wings and flew up into the trees, when he got to the top he saw nothing but more trees, but off in the distance, he saw what appeared to be a structure, but it was a long walk.

He slowly dropped from the tree as his wings started to hurt, he cringed as he folded his wings in, he decided to walk, but he had no choice now, it would be a long walk, but there wasn't any other option, he would need help, he wasn't sure how much longer he might last, each time he thought about it, his stomach would growl in hunger, and his throat would scream for water, he would have to hurry, or else he would surely pass out and die.

With a heavy sigh, he started walking in the direction of the building.

**A/N: well there you have it, the first chapter, hope you enjoyed and there will be more to come, in the future, see you all then.**


	2. Chapter 1

**A/N: manage to get out another chapter for this story, more chapters for this and other stories will be out in the next few days, hope you enjoy.**

**Legacy of the Alicorn's: chapter 1: a new life**

It was a bright day over the town of PonyVille, and ponies were well into their daily routines, vendors were selling their goods, store clerks bought and sold items, it was a very normal day for many, but some were hard at work.

(PonyVille, public library)

A young purple dragon was busy dusting a shelf of books, when he was done, he hopped off the ladder and looked around, smiling as the room seemed to shine, Twilight was out with Fluttershy and Rainbow Dash taking a flying lesson.

Despite her new wings, Twilight had a long way to go before she would be as great a flyer as her friends, but she was making great progress, just as he was finishing up, the front door opened with the familiar 'ding' sound.

He turned and saw a purple colored pony walk in, with a unhappy look on her face, he happily walked over to her, and gave a bow, "so, how was the flying lesson, princess" he said the last part slowly, Twilight gave a groan, "hard, do you know what it is like having two teachers with completely different teaching styles, Rainbow Dash says to push myself, but Fluttershy tells me to take it slow, uh, my wings will ache for weeks" she said extending her wings, and rubbing them.

Spike gave a light chuckle, as Twilight walked past her, "so can I get you anything, something to eat…" he said, but Twilight shook her head, "no, I think I'm going to take a nap, my entire body is sore" she said, Spike was about to say something, but suddenly his cheeks puffed up, and he burped out a large amount of green flames, when they evaporated, in front of him lay a neatly rolled up paper with a seal, keeping it closed, indicating that it was from Princess Celestia.

Spike picked it up, as Twilight walked over to him, Spike gave a quick skim, "what's it say, does she need me in Canterlot, the last meeting, was very boring, but I'll have to get used to it" she asked, Spike looked up at it, "yeah, I didn't read much, but it seems pretty important" he said and handed it to her, she levitated it up to her face and cleared her throat, and began to read out loud.

_Dear Princess Twilight._

_I trust your return to PonyVille has been pleasant, I can understand that the past few weeks have been very exhausting for you, adjusting to your new life and responsibilities, but I am writing to you for a different matter._

_I am writing this, because there is something very important we must speak about, being a Princess and an alicorn, it is time you learn the truth of our race, we have many important things to talk about, I ask that you come to Canterlot as soon as possible, your friends are more than welcome to come with you, but the meeting itself must be between us Princess's._

_We will await your arrival, _

_Yours truly Princess Celestia._

Twilight finished reading, and lowered the letter a shocked look on her face, she turned to Spike, who had a confused look on his face, "what did she mean by the 'truth of our race' it must be very important" he said, Twilight frowned, "yeah, alright, we'll leave by tomorrow morning, I suggest you get some sleep as well, I'm going to take a short nap, and we'll go see if any of our friends are able to join us" she said as she headed up the stairs, Spike quickly following her.

**A/N: well, there you have it, I apologize for it being a short chapter, but I promise the next one will be longer, hope you all enjoyed, and see you all next time.**


	3. Chapter 2

**A/N: hey guys, I'm back with another chapter for this story, I hope you have enjoyed it thus far, and there will be more chapters.**

**Legacy of the Alicorn's: chapter 2: history lesson**

(Canterlot, train station)

After receiving the letter from Celestia, Twilight and her friends immediately, made their way to the train station, and boarded the next train to Canterlot, judging by the seriousness of the note, Celestia would want to speak with Twilight as soon as possible, as the train pulled into the station of the capitol city, Twilight and her friends slowly got their things and made their way off the train, "so Twilight, what do you think Princess Celestia wants to talk to you about, from what you said, it seemed important" Rarity asked, as they walked on to the platform, Twilight shrugged, "I'm not sure, but she said she wanted to talk to me about the truth of our race, I had no idea Alicorn's existed aside from the Princess's" she said as they came to the front.

They saw a large carriage in front of them, a royal guard stepped down and opened the door, "greetings your highness, we have been instructed to bring you and your friends to the castle" he said, Twilight and her friends all looked up and saw Cadence sitting inside the carriage, obviously waiting again, she looked at Twilight and smiled, as they all climbed in, Cadence turned to Twilight, "Twilight, it's good to see you and your friends again, Celestia sent me to accompany you to the castle, we must get going, she's expecting you" she said as the door closed and carriage started making its way through the streets.

Along the ride, they mostly remained silent, Twilight decided to break the silence, "so Cadence, how are things in the empire?" Twilight asked, Cadence looked at her and smiled, "things are great, why do you ask?" she answered back, Twilight leaned back, "well I was just wondering, shouldn't you be there with Shining Armor, and why does Celestia want to speak with me so badly, what's this about, what truth of our race?" she asked, Cadence's smile fell, but she kept looking at Twilight, "Shining can run the empire for a few days, he is the prince after all, he sends his regards by the way, but as for why my aunt is calling you here, you'll just have to wait and see" she said in a solemn tone, and she turned to look out the window, Twilight turned to her friends, they all just shrugged their shoulders.

As the carriage pulled into the courtyard, the same royal guard jumped off and opened the door taking a bow as Twilight and Cadence stepped out, her friends quickly joined her, they all made her way to the main entrance, two more guards gave respectful bows, and opened the doors as the seven of them passed by.

It took a few minutes but when they eventually reached the door to the throne room, Cadence stopped for a minute, and turned to the others, primarily to Twilight, "Twilight, come with me, your friends will have to stay here, this meeting is strictly between Princess's" she said, Twilight nodded and turned to her friends, they all nodded as well, and Twilight followed Cadence into the throne room, the guards closing the doors behind them.

As they made their way to the middle of the room, Twilight looked to the left and saw Celestia standing in front of the window, staring out into the land, Cadence cleared her throat, and Celestia turned around and saw the two of them standing there, Celestia smiled as she made her way in front of Twilight, "it's good to see you again Twilight, I hope you had a nice trip" she said, Twilight did her best to smile, "indeed I did, but why can't my friends come in, what's this all about, I think I deserve some explanation" she said looking up at her former mentor, Celestia smiled, as the door behind them opened again, and in walked Princess Luna, she calmly walked past Twilight, and stood next to Celestia, Cadence walked past her as well, standing on the other side of Celestia, Twilight looked at all three of them.

"What is this about?" she asked, Celestia's smile faded, and she took a deep breath, "this is about you Twilight Sparkle, this is about you becoming an alicorn" she said, Twilight started to become worried, "what? Did I do something wrong, I'm practicing as hard as I can, really I am-" she said but was cut off by Celestia, "calm yourself, I assure you, you've done nothing wrong, you're here to learn the truth, the truth about our race, the alicorn's" she said, Twilight felt her anxiety leave her mind, only to be replaced with interest, "alicorn's? I thought you three were the only alicorn's alive today, are there more? Where have they been?" she kept asking, Celestia simply raised her hoof, silencing Twilight.

"Your right about one thing, we were the only three alicorn's, but at one time, there were hundreds of us, just as many alicorn's as they're were unicorns, or pegasi, or even earth ponies, back before the kingdom was created, during the time of the three tribes" she said making her way over to the window, she seemed distant for a moment, when Twilight, "then, how come I've never read about it at all, in any books" she said in confusion, Celestia sighed, "no, you wouldn't find anything on them, it happened many years ago when Luna and I were very young" she said turning back to Twilight, who was now fully focused on the story, Celestia cleared her throat, and sighed deeply, Twilight could tell, starting the story was troubling her, but she started none the less.

Celestia finally looked up, "it all started well over a thousand years ago, when the kingdom was not yet founded, there were four pony tribes, that argued over land, as you know in the story, but the fourth tribe was the alicorn's, a very powerful and wise race of ponies, they were very peaceful, they preferred to remain neutral to the other tribes, and not involve themselves with their affairs, everything was good for them, they all lived happy lives, free of war and death, their time was peaceful and plentiful, they devoted their days to studies and delving deeper into the art of magic, reaching levels of enlightenment, that no unicorn could dream of, but then, tragedy struck" she said sadness appearing in her eyes, Twilight listened intently, waiting for her to continue, Celestia took a deep breath and continued.

"a very powerful unicorn by the name of Bloodmane, saw the alicorn's as an impurity, he believed that the mixture of all three races was an abomination, he rallied hundreds of unicorns, pegasi, earth ponies alike, and set out to exterminate them, claiming it to be justice, many innocent lives lost at the strength of his army, murdering all of them, none were spared, not even foals, he ether killed them, or tortured them, severing their horns and wings, causing untold pain, murdering a son and daughter in front of their parents, the alicorn's tried to fight back, but even with their extensive knowledge, anypony who challenged Bloodmane, fell before him, soon it came to a point where almost every alicorn in existence had been wiped out" she said a single tear falling from her eye.

Twilight was shocked at what he was hearing, she knew there were some bad ponies in the world, but to be responsible for the deaths of thousands of innocent lives, it made her sick to her stomach, she watched as Celestia did her best to get control of herself, she watched as Luna walked over and comforted her sister, Twilight looked down, "wha…what happened to him, Bloodmane?" she asked, Celestia sighed and looked away for a minute, "supposedly, while hunting one of the few remaining alicorn's left, he disappeared, no trace of him or the alicorn he was chasing, vanished into thin air, never to be seen again, after his disappearance, his army began to fall apart, until the point where they separated, believing that they had killed them all, but as the decades and centuries past, rumors would spread of few surviving alicorn's that had gone into hiding, but they never came, the alicorn race seemed anything but dead, the rumors faded into legend, and eventually as the centuries past, the alicorn's faded into the past, lost to time, and so it has been for as long as we could remember" she said finally getting a hold of herself, Twilight felt her heart beat rapidly against her chest, trying to take in everything she was told, she had no idea, any of this had happened.

Twilight began to pace back and forth, "why wasn't I told sooner?" she asked, Celestia cleared her throat, "we wanted to wait until you were more adjusted to your new life, we didn't tell Cadence until she was of the right age, and able to understand our task" she said getting back to the middle of the room, Twilight looked up at her, "task?" she asked curiously, the other three alicorn's looked at each other solemn looks on their faces, Celestia cleared her throat, "we are the last four alicorn's in existence, for hundreds of years, we have protected our legacy, so that we might not entirely be forgotten to the sands of time, as an alicorn, it is also your duty to help preserve our legacy, Luna and I have done it for many centuries, then Cadence came along, and now you, we must do what we can, to make sure our legacy is secure, will you help us do this?" Celestia asked, eyes full of hope, Twilight looked down for a moment, not sure what to say, it was a very large task.

They waited patiently, and Twilight looked up and smiled, "I will" she said happily, they all smiled, and Twilight could see the look of relief on Celestia's face, Celestia smiled down at her, "good, it's been a long and tiring day for all of us, we should all get some rest" she said and they all made their way out of the room.

**A/N: well that was certainly interesting, hope you enjoyed, see you all next time, peace.**


	4. Chapter 3

**A/N: hey guys, it's been awhile since I wrote a chapter for this story, so I decided to get to it, and well…here's the next chapter, hope you all enjoy.**

**Legacy of the Alicorn's: chapter 3: captured**

The young alicorn walked quickly through the forest, not sure of his destination, all he knew was that he was headed towards the structure off in the distance; he hoped he was getting close, as he was getting weaker by the second.

As he walked, his head started hurting at certain points, causing him to fall down and garb his head, trying to stop the pain, memories began flashing through his mind, as it all started coming back to him, _"Rising Star, get out of here, go, run! Whatever you hear, don't stop, keep running" _he heard a male voice echo in his head, he knew who's voice it was, it was the voice of his father, right before he was killed.

The visions and memories passed through his mind, tears began spilling from his eyes, as the memory replayed in his head, he remembered running through the forest with his parents, them telling him to run, their dying screams, the ominous black coated figure standing over him, and bright flashing light, and then nothing, it all went black.

He cried out as he leaned up against a tree, tears running down his cheeks, he wiped them away and placed a hoof on his chest, trying to slow his breathing, he could feel his heart violently pounding against his chest, after taking a few minutes to calm himself, he pushed himself up, his hooves shaking, he steadied himself, and slowly started walking in the same direction again, his hooves becoming weaker each step.

Finally after a few more minutes of walking through the dense forest, he pushed through a large bush and looked around, he found himself inside a very large clearing in the forest, he scanned the clearing, and spotted the same structure he was looking for, a very tall building with a courtyard surrounded by a large wooden fence, with what appeared to be guard towers, he guessed it was some sort of militaristic structure, he had rather hoped to find a town, but this would probably be the closest piece of civilization he would find for another few miles, and he was pretty sure he would be able to make it much farther, due to his aching hooves, growling stomach, and dry throat.

He quickly started making his way towards the structure, hoping to find some help.

(Royal Guard outpost 22)

A young royal guard pony walked along the wall of the base, as part of his normal patrol route, his duty was to watch and warn of any signs of danger, not anything ever happened, aside from the occasional Timber wolf pack that would come near the base.

The many ponies who were assigned to this outpost, felt it to be the worst position, everything was always so dull and boring, very little action occurred, being stuck on a base in the middle of the Everfree Forest, always felt boring, half the time he didn't even know why he bothered, he never saw anything out of the ordinary, it was always the same, trees and plants, that was…until today.

As he walked along the wall, he glanced off into the distance, to the edge of the clearing, sometimes he would see Timber wolves stalking along the tree line, as is trying to find a way to get in, as he glanced off into the distance again, everything seemed to be as it was, quiet and boring, but as he glanced a third time, something caught his eye in the tree line.

He turned and narrowed his eyes, but it didn't help much, he quickly grabbed the binoculars that he had at his side, and brought it up to his eye's and looked through it, he watched the same area, as a young pony came walking out of the tree line and stood near the tree's for a second, he continued watching as the strange pony looked over at the structure, stood staring for a few seconds and started walking over slowly, he appeared to have a unicorn's horn, but as the guard continued to study him, he saw two bulges at his sides, under his cloak, from what he could tell, they appeared to be…the outline of a pair of wings.

He lowered the binoculars, a shocked looked on his face, he turned around and looked at the other guards pony, "um Lieutenant?" he asked, the other pony turned and looked up at him, "yes, what is it Private?" he asked, the Private looked back, and then glanced at the Lieutenant, "I caught something interesting, I think you should take a look" he said, the Lieutenant sighed and started making his way up the nearest ramp.

"Alright Private, what's so exciting?" he asked as he walked up to the Private, who just gave him the binoculars, and pointed in the direction, the Lieutenant took the binoculars and looked where he was pointing, his eyes rested on the stranger, slowly making his way towards the base, the Lieutenant lowered them, "hmm, there's never any ponies out this far, we're in the middle of the forest" he said raising the binoculars again, the Private cleared his throat, "that's not the only weird thing sir, he has a unicorn's horn…and what appears to be wings as well" he said, the Lieutenant turned to him, "what makes you say that?" he asked, the Private rubbed his head, "look at his sides, there's a bulge on each side, and the outline looks like wings" he said, the Lieutenant gave him a confused look, and then looked back through the binoculars, he looked at the pony's sides and saw what the Private was talking about, his eyes widened as he lowered them, "that's not possible…" he said with surprise, he thought for a minute before giving the Private his binoculars, "get a squad ready, let's go meet our new arrival" he said, as he walked back down the ramp, the Private quickly followed.

(Meanwhile…)

As Rising Star made his way closer to the building, he watched as the front gate opened, and a large number of ponies came running out, he gave a sigh of relief, as he thought they were here to save him, but as they got closer he saw that they were carrying spears, and they didn't seem too happy.

He stopped in place and waited for them to come to him, when they did, they broke off and ran around him, and closed behind him, forming a circle, and forcibly pointing their spears at him, "what is this?" he asked confused, but none of them answered, he turned and saw another pony walk through the circle, he had a uniform on, with a medal on it, Rising Star eyed him suspiciously, "what is the meaning of this, I demand to know what is going on, I've done nothing wrong" he said, the Lieutenant looked him over, walking up to him, he lifted Rising Star's cloak, and a shocked look appeared on his face, he put the cloak down and looked up at his horn, and then turned to him, "you are aware that this is a restricted area?" he asked, Rising Star looked around, "no I didn't, this is the middle of the forest, why would it be restricted?" he asked, the Lieutenant stared at him for a minute, "normally we would just turn you around, but in your case, it's different, the call is out of our hooves, we will need orders from the Princess's, you are a particularly interesting case, you'll need to come with us" he said as he began walking away, the soldiers gave a rough push, and Rising Star started walking with them, he had no idea what was going on, or what would happen to him, but he knew he could only wait for answer's.

**A/N: I apologize for taking such a long time with this one, but I just finished my session of summer school, so I will be free to do as much writing as possible, so you can all expect some more chapters for my stories in the coming weeks, thanks for being so patient, peace.**


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